GapMind for catabolism of small carbon sources

 

Finding step livF for L-phenylalanine catabolism in Marinobacter adhaerens HP15

5 candidates for livF: L-phenylalanine ABC transporter, ATPase component 1 (LivF)

Score Gene Description Similar to Id. Cov. Bits Other hit Other id. Other bits
hi HP15_3059 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 67% 98% 309.7 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 55% 253.4
med HP15_2703 branched-chain amino acid ABC transporter ATP-binding protein high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 52% 99% 241.9 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 53% 259.2
med HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein ABC transporter ATP-binding protein (characterized, see rationale) 44% 97% 207.2 Branched-chain amino acid transport system ATP-binding protein, component of The phenylpropeneoid uptake porter, CouPSTW 50% 212.2
med HP15_2877 ABC transporter, urea, ATP-binding protein, UrtE High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 43% 98% 169.1 UrtE, component of The high-affinity (<1 μM) urea porter 49% 191.0
med HP15_927 branched-chain amino acid ABC transporter, ATP-binding protein high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 37% 99% 160.6 ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM 35% 156.0

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

Also see fitness data for the candidates

Definition of step livF

Or cluster all characterized livF proteins

This GapMind analysis is from Aug 02 2021. The underlying query database was built on Aug 02 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory